"I was able to buy a delicious, super fresh tuna", the sushi chain owner said after the auction, as quoted by media.
The winning bid for the prized but threatened species at the predawn auction Saturday was more than double the 2013 annual New Year auction.
A bluefin tuna fetched a record 333.6 million yen ($3.1 million) at the first New Year's auction held at Tokyo's Toyosu fish market following the market's relocation from nearby Tsukiji last year.
"The celebration surrounding the annual Pacific bluefin auction hides how deeply in trouble this species really is", Jamie Gibbon, associate manager for global tuna conservation at The Pew Charitable Trusts, told the AP.
Self-described Japanese "Tuna King" Kiyoshi Kimura paid a record $3 million for a 612-pound (278-kilogram) bluefin tuna at the first new year's auction in Tokyo on Saturday.
This depletion could be one of the reasons the price of the tuna has gone up significantly - in previous years the fish has sold for £31 ($40) per pound, but this year's prices soared above £157 ($200) a pound.
Hundreds of sushi lovers queued for a taste.
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The Toyosu fish market opened in October after the famed Tsukiji market closed after 83 years of business.
The previous site at Tsukiji opened in 1935 and became the world's biggest fish market and a popular tourist attraction.
But the Japanese government, together with other countries, is backing plans to rebuild Pacific bluefin stocks of the fish, which is now depleted by 96 percent from their pre-industrial levels.
Tokyo governor Yuriko Koike, wearing white rubber boots, said: "I sincerely hope this market will be loved by many people".
But Toyosu is located on the site of a former gas plant and the soil was found to be contaminated, forcing local authorities to spend millions of dollars to clean it up and delaying the move.
In contrast, the new market, located around two kilometres to the east at Toyosu, boasts state-of-the-art refrigeration facilities and is almost twice as big as Tsukiji.